# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:48:43 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(2Z,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]\1[C@@H](O)[C@@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 OGN  OGN  'N-[(2Z,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)'  ligand  44  25  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OGN
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 OGN  CAA   C  C     0   0.503  -1.3810  -0.1458   0.0443
 OGN  CAB   C  CH1   0  -0.189  -2.5826  -1.0721   0.0805
 OGN  CAC   C  CH1   0   0.055  -3.7797  -0.4461  -0.6331
 OGN  CAD   C  CH1   0  -0.060  -3.9728   0.9814  -0.1284
 OGN  CAE   C  CH1   0  -0.011  -2.7147   1.7696  -0.4630
 OGN  CAF   C  CH2   0  -0.166  -2.7628   3.2018   0.0130
 OGN  CAH   C  CH3   0  -0.784  -1.6037  -4.6783  -0.4314
 OGN  NAI   N  NH1   0  -0.623  -2.2710  -2.3656  -0.4465
 OGN  OAJ   O  OH1   0  -0.657  -4.8820  -1.2682  -0.3902
 OGN  OAK   O  OH1   0  -0.666  -4.2327   0.9347   1.2498
 OGN  OAL   O  O2    0  -0.454  -1.5491   1.1665   0.1219
 OGN  OAM   O  OH1   0  -0.665  -1.6434   3.8840  -0.4924
 OGN  OAN   O  O     0  -0.496  -2.1289  -3.4318   1.5408
 OGN  NAO   N  NH1   0  -0.775   2.8988   0.7418   0.0857
 OGN  CAP   C  C     0   0.747   1.9998  -0.2569  -0.0886
 OGN  OAQ   O  O2    0  -0.407   0.7660   0.2667   0.0870
 OGN  OAR   O  O     0  -0.464   2.2285  -1.4064  -0.3585
 OGN  CAS   C  CR6   0   0.371   4.2914   0.6729  -0.0129
 OGN  CAT   C  CR16  0  -0.316   4.9941  -0.4253  -0.5097
 OGN  CAU   C  CR16  0  -0.245   6.3811  -0.3795  -0.5739
 OGN  CAV   C  CR16  0  -0.273   7.0874   0.7389  -0.1581
 OGN  CAW   C  CR16  0  -0.245   6.3841   1.8326   0.3300
 OGN  CAX   C  CR16  0  -0.342   5.0023   1.8014   0.4035
 OGN  NAY   N  N     0  -0.179  -0.2321  -0.6889   0.0423
 OGN  HAB   H  HCH1  0   0.309  -2.8482  -1.1991   1.1345
 OGN  HAC   H  HCH1  0   0.239  -3.5581  -0.3813  -1.7092
 OGN  HAD   H  HCH1  0   0.265  -4.8021   1.4387  -0.6855
 OGN  HAE   H  HCH1  0   0.258  -2.5913   1.7666  -1.5531
 OGN  HAF   H  HCH2  0   0.214  -3.7042   3.6345  -0.3512
 OGN  HAFA  H  HCH2  0   0.211  -2.7961   3.2283   1.1091
 OGN  HAH   H  HCH3  0   0.271  -0.5313  -4.8262  -0.2944
 OGN  HAHA  H  HCH3  0   0.266  -2.1096  -5.5522  -0.0255
 OGN  HAHB  H  HCH3  0   0.252  -1.8023  -4.6210  -1.4999
 OGN  HNAI  H  HNH1  0   0.403  -2.1053  -2.4365  -1.4382
 OGN  HOAJ  H  HOH1  0   0.459  -5.5947  -1.0110  -0.9837
 OGN  HOAK  H  HOH1  0   0.465  -4.6999   1.7319   1.5152
 OGN  HOAM  H  HOH1  0   0.460  -1.6692   4.7861  -0.1611
 OGN  HNAO  H  HNH1  0   0.418   2.5266   1.6372   0.3675
 OGN  HAT   H  HCR6  0   0.278   4.4809  -1.3094  -0.8500
 OGN  HAU   H  HCR6  0   0.259   6.9104  -1.2404  -0.9614
 OGN  HAV   H  HCR6  0   0.255   8.1675   0.7600  -0.2147
 OGN  HAW   H  HCR6  0   0.260   6.9104   2.7183   0.6611
 OGN  HAX   H  HCR6  0   0.271   4.4675   2.6606   0.7906
 OGN  CAG   C  C     0   0.528  -2.0275  -3.4453   0.3235

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 OGN  CAA  CAB   single    1.518  0.020  1.518
 OGN  CAA  OAL   single    1.325  0.020  1.325
 OGN  CAA  NAY   double    1.271  0.020  1.271
 OGN  CAB  CAC   single    1.528  0.020  1.528
 OGN  CAB  NAI   single    1.431  0.020  1.431
 OGN  CAC  CAD   single    1.526  0.020  1.526
 OGN  CAC  OAJ   single    1.396  0.020  1.396
 OGN  CAD  CAE   single    1.522  0.020  1.522
 OGN  CAD  OAK   single    1.403  0.020  1.403
 OGN  CAE  CAF   single    1.510  0.020  1.510
 OGN  CAE  OAL   single    1.437  0.020  1.437
 OGN  CAF  OAM   single    1.405  0.020  1.405
 OGN  CAG  CAH   single    1.507  0.020  1.507
 OGN  CAG  NAI   single    1.348  0.020  1.348
 OGN  CAG  OAN   double    1.222  0.020  1.222
 OGN  NAO  CAP   single    1.355  0.020  1.355
 OGN  NAO  CAS   single    1.398  0.020  1.398
 OGN  CAP  OAQ   single    1.352  0.020  1.352
 OGN  CAP  OAR   double    1.203  0.020  1.203
 OGN  OAQ  NAY   single    1.383  0.020  1.383
 OGN  CAS  CAT   aromatic  1.395  0.020  1.395
 OGN  CAS  CAX   aromatic  1.397  0.020  1.397
 OGN  CAT  CAU   aromatic  1.389  0.020  1.389
 OGN  CAU  CAV   aromatic  1.387  0.020  1.387
 OGN  CAV  CAW   aromatic  1.389  0.020  1.389
 OGN  CAW  CAX   aromatic  1.384  0.020  1.384
 OGN  CAB  HAB   single    0.970  0.020  1.090
 OGN  CAC  HAC   single    0.970  0.020  1.090
 OGN  CAD  HAD   single    0.970  0.020  1.090
 OGN  CAE  HAE   single    0.970  0.020  1.090
 OGN  CAF  HAF   single    0.970  0.020  1.090
 OGN  CAF  HAFA  single    0.970  0.020  1.090
 OGN  CAH  HAH   single    0.970  0.020  1.090
 OGN  CAH  HAHA  single    0.970  0.020  1.090
 OGN  CAH  HAHB  single    0.970  0.020  1.090
 OGN  NAI  HNAI  single    0.860  0.020  1.020
 OGN  OAJ  HOAJ  single    0.850  0.020  0.980
 OGN  OAK  HOAK  single    0.850  0.020  0.980
 OGN  OAM  HOAM  single    0.850  0.020  0.980
 OGN  NAO  HNAO  single    0.860  0.020  1.020
 OGN  CAT  HAT   single    0.930  0.020  1.080
 OGN  CAU  HAU   single    0.930  0.020  1.080
 OGN  CAV  HAV   single    0.930  0.020  1.080
 OGN  CAW  HAW   single    0.930  0.020  1.080
 OGN  CAX  HAX   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 OGN  NAY   CAA  OAL   122.54  3.000
 OGN  NAY   CAA  CAB   117.07  3.000
 OGN  OAL   CAA  CAB   120.17  3.000
 OGN  HAB   CAB  NAI   107.61  3.000
 OGN  HAB   CAB  CAC   107.89  3.000
 OGN  NAI   CAB  CAC   111.65  3.000
 OGN  HAB   CAB  CAA   106.62  3.000
 OGN  NAI   CAB  CAA   111.75  3.000
 OGN  CAC   CAB  CAA   111.05  3.000
 OGN  HAC   CAC  OAJ   111.33  3.000
 OGN  HAC   CAC  CAD   107.08  3.000
 OGN  OAJ   CAC  CAD   113.15  3.000
 OGN  HAC   CAC  CAB   108.85  3.000
 OGN  OAJ   CAC  CAB   107.22  3.000
 OGN  CAD   CAC  CAB   109.14  3.000
 OGN  HAD   CAD  OAK   111.84  3.000
 OGN  HAD   CAD  CAE   107.27  3.000
 OGN  OAK   CAD  CAE   112.73  3.000
 OGN  HAD   CAD  CAC   108.49  3.000
 OGN  OAK   CAD  CAC   108.48  3.000
 OGN  CAE   CAD  CAC   107.88  3.000
 OGN  HAE   CAE  OAL   108.19  3.000
 OGN  HAE   CAE  CAF   108.63  3.000
 OGN  OAL   CAE  CAF   107.20  3.000
 OGN  HAE   CAE  CAD   108.06  3.000
 OGN  OAL   CAE  CAD   111.33  3.000
 OGN  CAF   CAE  CAD   113.30  3.000
 OGN  HAFA  CAF  HAF   107.21  3.000
 OGN  HAFA  CAF  OAM   111.83  3.000
 OGN  HAF   CAF  OAM   111.86  3.000
 OGN  HAFA  CAF  CAE   109.81  3.000
 OGN  HAF   CAF  CAE   107.25  3.000
 OGN  OAM   CAF  CAE   108.77  3.000
 OGN  HAHB  CAH  HAHA  108.88  3.000
 OGN  HAHB  CAH  HAH   108.05  3.000
 OGN  HAHA  CAH  HAH   107.53  3.000
 OGN  HAHB  CAH  CAG   113.43  3.000
 OGN  HAHA  CAH  CAG   109.85  3.000
 OGN  HAH   CAH  CAG   108.93  3.000
 OGN  HNAI  NAI  CAG   118.41  3.000
 OGN  HNAI  NAI  CAB   117.50  3.000
 OGN  CAG   NAI  CAB   123.56  3.000
 OGN  HOAJ  OAJ  CAC   108.66  3.000
 OGN  HOAK  OAK  CAD   109.49  3.000
 OGN  CAE   OAL  CAA   119.64  3.000
 OGN  HOAM  OAM  CAF   108.08  3.000
 OGN  HNAO  NAO  CAS   115.51  3.000
 OGN  HNAO  NAO  CAP   116.42  3.000
 OGN  CAS   NAO  CAP   128.00  3.000
 OGN  OAR   CAP  OAQ   124.96  3.000
 OGN  OAR   CAP  NAO   127.39  3.000
 OGN  OAQ   CAP  NAO   107.66  3.000
 OGN  NAY   OAQ  CAP   112.76  3.000
 OGN  CAX   CAS  CAT   119.05  3.000
 OGN  CAX   CAS  NAO   116.49  3.000
 OGN  CAT   CAS  NAO   124.45  3.000
 OGN  HAT   CAT  CAU   119.21  3.000
 OGN  HAT   CAT  CAS   121.23  3.000
 OGN  CAU   CAT  CAS   119.56  3.000
 OGN  HAU   CAU  CAV   119.98  3.000
 OGN  HAU   CAU  CAT   118.60  3.000
 OGN  CAV   CAU  CAT   121.42  3.000
 OGN  HAV   CAV  CAW   120.57  3.000
 OGN  HAV   CAV  CAU   120.58  3.000
 OGN  CAW   CAV  CAU   118.85  3.000
 OGN  HAW   CAW  CAX   119.20  3.000
 OGN  HAW   CAW  CAV   120.38  3.000
 OGN  CAX   CAW  CAV   120.43  3.000
 OGN  HAX   CAX  CAW   119.59  3.000
 OGN  HAX   CAX  CAS   119.72  3.000
 OGN  CAW   CAX  CAS   120.69  3.000
 OGN  OAQ   NAY  CAA   110.93  3.000
 OGN  OAN   CAG  NAI   123.04  3.000
 OGN  OAN   CAG  CAH   122.12  3.000
 OGN  NAI   CAG  CAH   114.84  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 OGN  CONST_01  CAV   CAU  CAT  CAS    0.00   0.0  0
 OGN  CONST_02  CAV   CAW  CAX  CAS    0.00   0.0  0
 OGN  CONST_03  CAW   CAX  CAS  CAT    0.00   0.0  0
 OGN  CONST_04  CAW   CAV  CAU  CAT    0.00   0.0  0
 OGN  CONST_05  CAX   CAS  CAT  CAU    0.00   0.0  0
 OGN  CONST_06  CAX   CAW  CAV  CAU    0.00   0.0  0
 OGN  CONST_07  CAU   CAT  CAS  NAO  180.00   0.0  0
 OGN  CONST_08  CAW   CAX  CAS  NAO  180.00   0.0  0
 OGN  CONST_09  HAU   CAU  CAT  CAS  180.00   0.0  0
 OGN  CONST_10  HAW   CAW  CAX  CAS  180.00   0.0  0
 OGN  CONST_11  HAX   CAX  CAS  CAT  180.00   0.0  0
 OGN  CONST_12  HAV   CAV  CAU  CAT  180.00   0.0  0
 OGN  CONST_13  HAT   CAT  CAU  CAV  180.00   0.0  0
 OGN  CONST_14  CAT   CAS  NAO  CAP    0.00   0.0  0
 OGN  CONST_15  CAX   CAS  NAO  CAP  180.00   0.0  0
 OGN  CONST_16  HNAO  NAO  CAS  CAT  180.00   0.0  0
 OGN  CONST_17  CAH   CAG  NAI  CAB  180.00   0.0  0
 OGN  CONST_18  OAN   CAG  NAI  CAB    0.00   0.0  0
 OGN  CONST_19  CAS   NAO  CAP  OAQ  180.00   0.0  0
 OGN  CONST_20  CAS   NAO  CAP  OAR    0.00   0.0  0
 OGN  CONST_21  HNAI  NAI  CAG  CAH    0.00   0.0  0
 OGN  Var_01    NAY   CAA  OAL  CAE  151.87  30.0  1
 OGN  Var_02    HAH   CAH  CAG  NAI  104.95  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OGN  chir_01  CAB  CAA  CAC  NAI  negativ
 OGN  chir_02  CAC  OAJ  CAB  CAD  positiv
 OGN  chir_03  CAD  OAK  CAE  CAC  negativ
 OGN  chir_04  CAE  OAL  CAD  CAF  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 OGN  plan-1  NAO   0.020
 OGN  plan-1  CAS   0.020
 OGN  plan-1  CAT   0.020
 OGN  plan-1  CAU   0.020
 OGN  plan-1  CAV   0.020
 OGN  plan-1  CAW   0.020
 OGN  plan-1  CAX   0.020
 OGN  plan-1  HAT   0.020
 OGN  plan-1  HAU   0.020
 OGN  plan-1  HAV   0.020
 OGN  plan-1  HAW   0.020
 OGN  plan-1  HAX   0.020
 OGN  plan-2  NAO   0.020
 OGN  plan-2  CAP   0.020
 OGN  plan-2  CAS   0.020
 OGN  plan-2  HNAO  0.020
 OGN  plan-3  CAB   0.020
 OGN  plan-3  CAH   0.020
 OGN  plan-3  NAI   0.020
 OGN  plan-3  OAN   0.020
 OGN  plan-3  HNAI  0.020
 OGN  plan-3  CAG   0.020
 OGN  plan-4  NAO   0.020
 OGN  plan-4  CAP   0.020
 OGN  plan-4  OAQ   0.020
 OGN  plan-4  OAR   0.020

